For full color PNG

For graphic formats, make sure when you load it, select the appropriate setting in the color channel setting to convert it into black and white images and allow labeling.

Make sure you know the dimension and set it properly to stack it well

X and Y dimensions are defined by the 2D slices or pictures you acquired.

Z dimension is defined via the number of pictures you stacked together.

However, you still need to take the VOXEL dimension into consideration.

If the readme files tell you that the XYZ resolutions are IDENTITICAL, then you have a CUBIC voxel. X = 0.33mm, Y = 0.33mm, Z = 0.33mm then X:Y:Z ratio = 1:1:1

If the readme files tell you that XYZ resolution are NOT identical, they you have a NON-cubic voxel and you need to adjust Z-stacking accordingly. X = 0.33mm, Y = 0.33mm, Z = 4mm then X:Y:Z ratio = 1:1:12

Example 1:

You have a stack of 50 images with dimension 900*1000

The voxel is a CUBE, eg. x:y:z = 1:1:1

To define boundary: X = 900, Y = 1000, Z = 50

Example 2:

You have a stack of 200 images with dimension 130*300

The voxel is NOT a cube but with ratio of X,Y,Z = 1:1:2

To define the boundary: X = 130, Y = 300, Z = 400

For MRI

* Look under Root\Radiologicla\MRI\
* T1, T2, POC and PD all have different meanings
* All files are in RAW format when reading from Amira.
* They are taken from every 4mm where as PNG or RAW scans are taken every 0.33mm
* Read the mriHeaders folder for detailed explanation on each individual files
* Dimensions:
o X = 256
o Y = 256
o Z = how many slices you selected to load up
o Header = 7900 most of the time. "Requested" does not match "filesize" then use "filesize" - "requested" when no "header" = 0
o Anyway, your goal to load things up properly, is to make requested = filesize.
* Datatype: most of the time leave it at ushort or short.
* Voxel size is usually:
o X = 0.859375 mm
o Y = 0.859375 mm
o Z = 4 mm
o